biogems.info - gems for bioinformatics

New: CloudBioLinux packages are now listed on biogems.info !

#	biogem	description	by	version	released	stars	issues	total	7d	90d**)
								downloads	commits
1	bio	Bioinformatics library (...)	BioRuby project	1.4.3.0001	11 months	30	18	60090
2	biodiversity	Parser of scientific names (...)	Dmitry Mozzherin	3.1.4	4 months	10	5	33337	0	0
3	bio gem	Biogem is a software generator for Ruby in (...)	Raoul J.P. Bonnal, Pjotr Prins	1.3.5	8 months	14	11	27560	0	0
4	bio samtools	Binder of samtools for Ruby, on the top (...)	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	2.0.3	1 day	15	4	21664	8	36
5	entrez	Http requests to entrez e-utilities (...)	Jared Ning	0.5.8.1	2 years	4	...	17685	0	0
6	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome (...)	Hiroyuki Mishima, Jan Aerts	0.6.2	3 weeks	13	1	17023	0	15
7	intermine	Webservice client library for intermine data-warehouses (...)	Alex Kalderimis	1.04.00	9 months			16301
8	bio gadget	Gadgets for bioinformatics (...)	Shintaro Katayama	0.4.8	10 months		...	14374	0	0
9	sequenceserver	Blast search made easy! (...)	Anurag Priyam, Ben J Woodcroft, Yannick Wurm	0.8.7	12 weeks	30	30	14154	0	10
10	bio gff3	Gff3 parser for big data (...)	Pjotr Prins	0.9.1	20 months	6	2	14087	0	0
11	bio maf	Maf parser for BioRuby (...)	Clayton Wheeler	1.0.1	20 months	10	30	12042	0	0
12	bio logger	Log4r wrapper with extra features for roles and (...)	Pjotr Prins	1.0.1	2 years	4	2	10287	0	0
13	bio grid	A biogem to submit jobs on a queue (...)	Francesco Strozzi	0.3.3	18 months	5	...	10145	0	0
14	bio svgenes	Create pretty svg-format images of features, gene models (...)	Dan MacLean	0.4.1	3 months	7	5	9170	0	0
15	bio blastxmlparser	Very fast blast xml parser and library for (...)	Pjotr Prins	1.1.1	14 months	9	...	8197	0	0
16	bio faster	A fast parser for fastq files (...)	Francesco Strozzi	0.4.5	22 months	9	...	7905
17	bio alignment	Support for multiple sequence alignments (msa) (...)	Pjotr Prins	0.0.7	22 months	6	4	7398	0	0
18	bio phyta	Pipeline to remove contaminations from est libraries (...)	Philipp Comans	0.9.4	2 years	1	1	7008
19	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha (...)	George Githinji	0.7.1	14 months	1	...	6675
20	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv (...)	Pjotr Prins	0.9.0	7 weeks	8	20	6668	0	26
21	scaffolder	Build genome output files (...)	Michael Barton	0.5.0	8 months		...	6482
22	bio assembly	BioRuby assembly plugin (...)	Chase Miller, Francesco Strozzi	0.1.0	3 years	4	...	6271
23	bio bigbio	Low memory sequence emitters (...)	Pjotr Prins	0.1.5	11 months	8	1	6055	0	0
24	genfrag	This is a development release (...)	Pjotr Prins and Trevor Wennblom	0.0.0.4	4 years			5814
25	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org) (...)	Rutger Vos, Anurag Priyam	1.1.0	23 months	6	1	5776	0	0
26	eutils	Lightweight Ruby api for ncbi eutils (...)	Joon Lee, aka seouri	0.2.1	9 months	6	...	5719	0	0
27	bio signalp	A wrapper for the signal peptide prediction algorith (...)	Ben J Woodcroft	0.3.0	20 months	1	...	5685	0	0
28	bio tm hmm	A BioRuby plugin for interaction with the transmembrane (...)	Ben J. Woodcroft	0.2.2	16 months	2	...	5566	0	0
29	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point (...)	George Githinji, Pascal Betz	0.1.3	2 years	3	...	5543	0	0
30	bio graphics	Library for visualizing genomic regions (...)	Jan Aerts	1.4	6 years			5477
31	bio sambamba	Ruby wrapper for sambamba tool (...)	Artem Tarasov	0.0.5	20 months	2	...	5266	0	0
32	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps (...)	Hiroyuki Mishima	0.1.2	3 years	3	...	5163	0	0
33	biointerchange	An open source framework for transforming heterogeneous data (...)	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.1	8 months	7	3	5049	0	10
34	bio ngs	Bio-ngs provides a framework for handling ngs data (...)	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	22 months	27	14	5014	0	0
35	bio kmer counter	A biogem for counting small kmers for fingerprinting (...)	Ben J Woodcroft	0.1.2	10 months	5	...	4903	0	0
36	bio octopus	Running and parsing of the protein transmembrane domain (...)	Ben J Woodcroft	0.1.1	2 years	1	...	4802	0	0
37	bio band	Data mining algorithms for jRuby (...)	arrigonialberto86	0.1.11	7 months	12	3	4599	0	0
38	goruby	Gene ontology (go) interface for Ruby (...)	Ben J Woodcroft	0.2.0	3 years	8	...	4261
39	bio bwa	Ruby binding for bwa mapping software (...)	Francesco Strozzi	0.2.2	3 years	3	...	4071	0	0
40	ruby ensembl api	Api to ensembl databases (...)	Jan Aerts, Francesco Strozzi	1.0.1	3 years	30	4	4008	0	0
41	bio lazyblastxml	A plugin that allows you to parse large (...)	robsyme	0.4.0	2 years	1	...	3900
42	bio bgzf	Reading/writing bgzf blocks (...)	Artem Tarasov, Clayton Wheeler	0.2.1	20 months	2	...	3884	0	0
43	bio pileup iterator	Iterate through a samtools pileup file (...)	Ben J. Woodcroft	0.0.4	17 months	1	...	3707	0	0
44	bio cd hit report	Read and manipulate cd-hit clusters (...)	George Githinji	0.1.0	11 months	2	1	3269
45	bio kb illumina	Geneexpression illuminahumanannotation (...)	Raoul J.P. Bonnal	0.1.0	3 years	1	...	3206	0	0
46	bio plasmoap	Implementation of the plasmoap algorithm (...)	Ben J Woodcroft	0.0.2	2 years	1	...	3173	0	0
47	bio tabix	Ruby binding for samtools tabix (...)	throwern	1.0.1	6 months	3	...	2932	0	0
48	bio gff3 pltools	Ruby wrapper for the gff3-pltools (...)	Marjan Povolni	0.3.0	20 months			2890
49	bio rdf	Bioinformatics triple-store support (...)	Pjotr Prins	0.0.2	23 months	4	1	2887	0	27
50	bio affy	Parse affymetrix cel/cdf files (...)	Pjotr Prins	0.5.1	2 years	2	1	2830
51	bio chembl	Chembl rest api client, parser and container (...)	Mitsuteru Nakao	0.1.3	21 months	1	1	2818	0	0
52	bio ucsc util	Ruby binding to the ucsc kent utilities (...)	throwern	0.1.2	18 months	1	...	2800	0	0
53	bio gngm	Next-generation mapping of mutations (...)	Dan MacLean	0.2.1	16 months	2	...	2791	0	0
54	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser, (...)	Raoul J.P. Bonnal	0.0.1	2 years	1	...	2667	0	0
55	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal (...)	Ben J. Woodcroft	0.3.0	23 months	1	...	2479	0	0
56	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be (...)	Ben J Woodcroft	0.0.3	2 years	1	...	2438	0	0
57	bio basespace sdk	Basespace Ruby sdk is a Ruby based software (...)	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	8 months	8	2	2379
58	bio hmmer model	Parse pfam hmm definition files (...)	Ben J. Woodcroft	0.0.2	23 months	1	...	2089	0	0
59	bio unichem	BioRuby plugin for unichem rest web service (...)	Mitsuteru Nakao	0.3.0	14 months		...	2037
60	bio protparam	A protparam compatible utility for BioRuby (...)	hryk	0.2.0	15 months	1	...	2035	0	6
61	bio gag	Bio-gag is a biogem for detecting and correcting (...)	Ben J Woodcroft	0.1.0	17 months	2	...	1940
62	bio synreport	Reports whether a nucleotide change results in synonymous (...)	Dan MacLean	0.1.2	11 months		...	1914	0	0
63	bio krona	This biogem is built around krona, a flashy (...)	Ben J. Woodcroft	0.1.1	8 months	1	...	1894	0	0
64	bio statsample timeseries	Timeseries modules for statsample (...)	Ankur Goel, Claudio Bustos	0.2.1	6 months		...	1730
65	bio sge	BioRuby plugin for sun grid engine (...)	Toshiaki Katayama	0.0.0	3 years	4	...	1670	0	0
66	bio hello	Hello world plugin for the BioRuby (just for (...)	Toshiaki Katayama	0.0.0	3 years	3	...	1650
67	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns (...)	Trevor Wennblom	1.0.0	2 years		1	1649	0	0
68	dna sequence aligner	Does high pairwise alignment of sequencing reads with (...)	John T. Prince	0.0.2	4 years			1627
69	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of (...)	Ben J Woodcroft	0.1.0	3 years	1	...	1401	0	0
70	bio core ext	BioRuby core ext: plugins which require external library (...)	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	2 years	1	...	1398	0	0
71	bio data restriction enzyme	Restriction enzyme dataset (...)	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	2 years		...	1357	0	0
72	bio biolinux	Meta package for biolinux distribution (...)	Raoul J.P. Bonnal	0.1.0	2 years	2	...	1344
73	bio ensembl	A Ruby api to the ensembl database (...)	Jan Aerts, Francesco Strozzi	1.1.0	2 years	3	...	1336	0	0
74	bio foo	One-line summary of your gem (...)	Toshiaki Katayama	0.0.0	2 years	1	...	1330
75	bio dbsnp	Decoding the dbsnp bitfield (...)	Hiroyuki Mishima	0.1.1	2 years	2	...	1297	0	0
76	bio phyloxml	Phyloxml plugin for BioRuby (...)	Diana Jaunzeikare, Clayton Wheeler	0.9.0	23 months	3	...	1290	0	0
77	bio exportpred	Wrapper around the exportpred algorithm for predicting p (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1275	0	0
78	bio aliphatic index	A simple biogem that allows computation of the (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1257	0	0
79	bio hydropathy	Hydropathy scale for BioRuby (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1239
80	publisci	Publish scientific results to the semantic web (...)	Will Strinz	0.1.5	5 months	3	16	1172	0	3
81	intermine bio	Biological extensions for the intermine webservice client library (...)	Alex Kalderimis	0.98.1	2 years			1137
82	bio hmmer3 report	Enables parsing of hmmer version 3 reports (...)	Christian Zmasek, Ben J Woodcroft	0.0.1	23 months	1	1	1116	0	0
83	bio incanter	Build graph with jRuby (...)	Matteo Picciolini	0.1.0	20 months		...	1040
84	bio ipcress	A programmatic interface to the ipcress in-silico pcr (...)	Ben J Woodcroft	0.0.1	20 months	1	...	1019	0	0
85	bio gggenome	Gggenome Ruby client (...)	Mitsuteru Nakao	0.2.0	8 months	1	...	944
86	bio ensembl rest	Ruby ensembl rest api (...)	Alberto Donizetti	0.2.0	6 months	3	...	866	0	0
87	bio statsample glm	Generalized linear models for statsample (...)	Ankur Goel	0.1.1	6 months		...	821
88	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata (...)	Ben J. Woodcroft	0.0.1	15 months		...	789	0	0
89	bio velvet	Parser to work with file formats used in (...)	Ben J Woodcroft	0.2.0	2 weeks		...	678	0	7
90	bio stockholm	Parse stockholm sequence alignment format (...)	Ben J. Woodcroft	0.0.1	10 months	2	...	569	0	0
91	bio liftover	Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...) new	Andrei Rozanski	1.3.0	5 weeks		...	537
92	bio commandeer	Dead simple method of running shell commands from (...)	Ben J. Woodcroft	0.1.0	3 months		...	531	0	0
93	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood (...)	Fernando Izquierdo	0.1.0	9 months		...	507	0	0
94	bio express beta diversity	Interface for express beta diversity (...)	Ben J. Woodcroft	0.1.0	2 months		...	497
95	bio repeatmasker	Bio-repeatmasker (...)	Andrei Rozanski	0.0.3	3 months			495
96	bio vcf	Vcf parser (...)	Pjotr Prins	0.0.2	6 weeks		1	399	0	83
97	bio cigar	A parser for cigar format alignments (...)	Ben J Woodcroft	0.1.0	7 weeks	1	...	335
98	bio qtlHD	(...) pre		pre				333
99	bio biostars analytics	Biostars data-mining and statistical analysis (...) new	Joachim Baran	0.2.0	1 week		...	287	0	16
100	bio exominer	Mine publications for gene names (...)	Pjotr Prins	0.0.3	7 weeks		...	164	0	19
101	genomichdt	A restful service for sharing genomic data (...)	Joachim Baran, Robert Buels, Michel Dumontier	0.0.1	5 weeks	2	...	136
102	bio velvet underground	Bindings to some internals of the velvet assembler (...) new	Ben Woodcroft	0.0.1	2 weeks		...	113	4	17
103	bio polyploid tools	Tool to work with polyploids, ngs and molecular (...) new	Ricardo H. Ramirez-Gonzalez	0.1.0	2 weeks		...	111	0	25
104	bio primer3	(...) new		pre				54

*) gem downloads (total & last 90 days) from rubygems.org as of 2014-04-19
**) number of commits on GitHub (last 7 days & last 90 days)